SAXSdb — 1kxo

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DigA16

Pieris brassicae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 16–189	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；0.1-M Hepes, 10% Isopropanole, 19% PEG 4000, pH = 7.8, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.289

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1KXO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BBP MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION. Deposited 1990-09-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 16–188（173 aa） Chain B 16–188（173 aa） Chain C 16–188（173 aa） Chain D 16–188（173 aa）	Not recorded	BLV BILIVERDIN IX GAMMA CHROMOPHORE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1LKE ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN Deposited 2002-04-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	DOG DIGOXIGENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1-M HEPES, 10% ISOPROPANOL, 19% PEG 4000, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.248
1LNM ANTICALIN DIGA16 IN COMPLEX WITH DIGITOXIGENIN Deposited 2002-05-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	DTX DIGITOXIGENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.1-M hepes, 10% isopropanol, 19% peg 4000, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.245
1N0S ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN Deposited 2002-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；2.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK	Resolution 2.00 Å R-free 0.243
1N0S ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN Deposited 2002-10-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–189（174 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；2.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK	Resolution 2.00 Å R-free 0.243
1T0V NMR Solution Structure of the Engineered Lipocalin FluA(R95K) Northeast Structural Genomics Target OR17 Deposited 2004-04-13	Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：R95K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 150 mM NaCl; 10 mM Na-PO4; 50 mM benzamidine; 0.2 mM EDTA；Pressure ambient NMR sample composition 0.7 mM FluA(R95K) U-13C,15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) U-50% 2H,15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) U-15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 100% D2O NMR sample composition 0.7 mM FluA(R95K) 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BBP_PIEBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–174； UniProt 16–189

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1kxo
Deposition date deposition_date	2002-02-01
Structure title title	ENGINEERED LIPOCALIN DIGA16 : APO-FORM
Keywords keywords	pieris brassicae, lipocalin, anticalin, genetical engineering, digoxigenin, LIGAND BINDING PROTEIN; LIGAND BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	16.70 Å
Radius of gyration Rg (electron density) rg_electron	15.38 Å
Forward intensity I(0) i0	6518990.00
Molecular weight molecular_weight	18663.0 kDa
Excluded volume excluded_volume	23377 Å³
Envelope volume envelope_volume	27159 Å³
Hydration-shell volume shell_volume	14817 Å³
Envelope diameter envelope_diameter	49.2 Å
Shell Rg shell_rg	21.32 Å
Envelope Rg envelope_rg	15.66 Å
Shape Rg shape_rg	15.33 Å
Total Rg total_rg	16.65 Å
Total atoms total_atoms	1320
Residues n_residues	165
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	51.0 Å
Rg (real space) rg_real	16.57 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	6.5190e+06
I(0) uncertainty (real space) i0_real_error	7.4730e+04
Rg (reciprocal space) rg_reciprocal	16.58 Å
I(0) (reciprocal space) i0_reciprocal	6519000.0000
Solution quality estimate total_estimate	0.8993
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.050
Kurtosis Kurtosis kurtosis	-0.443
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1104000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.996

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kxoa_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (1 domains)

Domain ID domain_id	1kxoA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

▶

8. Citations (3)

▶

Unit-cell length a length_a	73.873 Å
Unit-cell length b length_b	63.476 Å
Unit-cell length c length_c	38.191 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	48.220 Å
R factor r_factor	0.2123
R_work r_work	0.2090
R_free r_free	0.2890

Description description	DigA16
Molecular weight formula_weight	20833.2 kDa
Mutation mutation	N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1424

ENGINEERED LIPOCALIN DIGA16 : APO-FORM

1. Protein Identity and Related Structures Protein Identity & Related Structures

DigA16

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Pieris brassicae
通用名 common_name	large cabbage white
NCBI Class编号 ncbi_taxonomy_id	7116
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	104

fit	/app/data/saxs_computation/kx/1kxo/1kxo.fit
pddf	/app/data/pr_computation/kx/1kxo/1kxo.pr.out
profile	/app/data/saxs_computation/kx/1kxo/1kxo.dat